PDB-8gdw: Crystal structure of Domain Related to Iron (DRI) from cyanobacteria

ID or keywords:

Entry

Database: PDB / ID: 8gdw

Title

Crystal structure of Domain Related to Iron (DRI) from cyanobacteria

Components

Ssr1698 protein

Keywords

METAL BINDING PROTEIN / Heme binding protein / DUF2470 / heme homeostasis / succinate dehydrogenase / zinc and heme binding sites

Function / homology

Domain of unknown function DUF2470 / Domain of unknown function (DUF2470) / Haem oxygenase HugZ-like superfamily / metal ion binding / Ssr1698 protein

Function and homology information

Biological species

Synechocystis sp. PCC 6803 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.35 Å

Authors

Kumaran, D. / Grosjean, N. / Blaby, E.C.

Funding support

United States, 1items

Citation

Journal: Nat Commun / Year: 2024
Title: A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria.
Authors: Grosjean, N. / Yee, E.F. / Kumaran, D. / Chopra, K. / Abernathy, M. / Biswas, S. / Byrnes, J. / Kreitler, D.F. / Cheng, J.F. / Ghosh, A. / Almo, S.C. / Iwai, M. / Niyogi, K.K. / Pakrasi, H.B. ...

History

Deposition	Mar 6, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 13, 2024	Provider: repository / Type: Initial release
Revision 1.1	Apr 24, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8gdw.cif.gz	93.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8gdw.ent.gz		Display	PDB format
PDBx/mmJSON format	8gdw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8gdw_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	8gdw_full_validation.pdf.gz	1.8 MB	Display
Data in XML	8gdw_validation.xml.gz	15.6 KB	Display
Data in CIF	8gdw_validation.cif.gz	21.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gd/8gdw ftp://data.pdbj.org/pub/pdb/validation_reports/gd/8gdw	HTTPS FTP

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Related structure data

Related structure data	8fm6C 8gbkC 8gf4C 5bncS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

AAA: Ssr1698 protein

BBB: Ssr1698 protein

CCC: Ssr1698 protein

DDD: Ssr1698 protein

hetero molecules

45.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	51.716, 87.230, 57.241
Angle α, β, γ (deg.)	90.000, 94.981, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Ssr1698 protein / Domain Related to Iron / DRI Mass: 11306.716 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: ssr1698 / Production host: Escherichia coli (E. coli) / References: UniProt: P73129
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.84 Å³/Da / Density % sol: 56.75 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEG3350, 100 mM Bis-Tris, pH 5.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 15, 2019
Radiation	Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 2.35→29.5 Å / Num. obs: 20972 / % possible obs: 99 % / Redundancy: 5.3 % / B_iso Wilson estimate: 56.6 Å² / CC_1/2: 0.99 / R_merge(I) obs: 0.055 / Net I/σ(I): 15
Reflection shell	Resolution: 2.35→2.41 Å / Redundancy: 5 % / R_merge(I) obs: 0.736 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1362 / CC_1/2: 0.76 / % possible all: 87.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
autoPROC		data reduction
autoPROC		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 5BNC

5bnc

Resolution: 2.35→29.5 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.945 / SU B: 8.899 / SU ML: 0.203 / Cross valid method: FREE R-VALUE / ESU R: 0.308 / ESU R Free: 0.235

	R_factor	Num. reflection	% reflection
R_free	0.2474	1027	4.901 %
R_work	0.197	19927	-
all	0.199	-	-
obs	-	20954	98.989 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 61.989 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.376 Å²	0 Å²	2.54 Å²
2-	-	-3.183 Å²	-0 Å²
3-	-	-	3.069 Å²

Refinement step

Cycle: LAST / Resolution: 2.35→29.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3096	0	4	34	3134

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	3140
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.016	2952
X-RAY DIFFRACTION	r_angle_refined_deg	1.545	1.638	4240
X-RAY DIFFRACTION	r_angle_other_deg	1.341	1.584	6824
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.696	5	400
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.667	25.122	164
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.944	15	560
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.056	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.059	0.2	432
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3624
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	656
X-RAY DIFFRACTION	r_nbd_refined	0.21	0.2	686
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.203	0.2	2654
X-RAY DIFFRACTION	r_nbtor_refined	0.161	0.2	1524
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.089	0.2	1564
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.138	0.2	59
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.113	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.085	0.2	11
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.224	0.2	31
X-RAY DIFFRACTION	r_nbd_other	0.24	0.2	85
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.148	0.2	7
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.011	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	5.425	6.375	1612
X-RAY DIFFRACTION	r_mcbond_other	5.427	6.374	1611
X-RAY DIFFRACTION	r_mcangle_it	8.181	9.556	2008
X-RAY DIFFRACTION	r_mcangle_other	8.178	9.556	2009
X-RAY DIFFRACTION	r_scbond_it	5.644	6.855	1528
X-RAY DIFFRACTION	r_scbond_other	5.642	6.855	1529
X-RAY DIFFRACTION	r_scangle_it	8.698	10.028	2232
X-RAY DIFFRACTION	r_scangle_other	8.696	10.028	2233
X-RAY DIFFRACTION	r_lrange_it	12.529	75.701	3332
X-RAY DIFFRACTION	r_lrange_other	12.529	75.687	3331

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.35-2.41	0.323	75	0.299	1281	X-RAY DIFFRACTION	87.7
2.411-2.477	0.292	80	0.272	1474	X-RAY DIFFRACTION	100
2.477-2.549	0.319	72	0.251	1371	X-RAY DIFFRACTION	100
2.549-2.627		71		1352	X-RAY DIFFRACTION	99.8596
2.627-2.713	0.325	81	0.244	1333	X-RAY DIFFRACTION	100
2.713-2.808	0.338	80	0.234	1243	X-RAY DIFFRACTION	100
2.808-2.914	0.291	65	0.224	1245	X-RAY DIFFRACTION	100
2.914-3.033	0.282	64	0.225	1173	X-RAY DIFFRACTION	100
3.033-3.167	0.335	67	0.225	1147	X-RAY DIFFRACTION	100
3.167-3.321	0.261	47	0.222	1077	X-RAY DIFFRACTION	99.9111
3.321-3.5	0.275	55	0.216	1064	X-RAY DIFFRACTION	100
3.5-3.712	0.28	46	0.205	978	X-RAY DIFFRACTION	99.7079
3.712-3.967	0.243	44	0.192	924	X-RAY DIFFRACTION	100
3.967-4.283	0.252	45	0.167	856	X-RAY DIFFRACTION	100
4.283-4.689	0.179	36	0.151	815	X-RAY DIFFRACTION	100
4.689-5.238	0.254	22	0.171	731	X-RAY DIFFRACTION	100
5.238-6.04	0.2	30	0.195	634	X-RAY DIFFRACTION	100
6.04-7.377	0.165	25		558	X-RAY DIFFRACTION	99.4881
7.377-10		14		430	X-RAY DIFFRACTION	99.3289

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